Biodiesel is one of the most popular biofuels as it is a promising substitute of the conventional diesel fuel, but for now it cannot be used as a stand-alone fuel due to its low oxidative stability. For this reason, the last years there have been efforts for its upgrading through the partial hydrogenation of the fatty acid methyl esters (FAMEs) that biodiesel consists of. This procedure succeeds in resolving the problem of low oxidative stability, but in some cases a new problem arises as the non-selective hydrogenation is deteriorating the fuel’s cold flow properties, which are crucial for its operation without damaging the vehicle’s engine. More specifically, the problem of deteriorated cold flow properties is caused by the formation of trans-monounsaturated FAMEs and fully saturated FAMEs while the hydrogenation reaction is taking place. The hydrogenated biodiesels are preferred to contain more cis-monounsaturated FAMEs, because these are considered to have the best combination between high oxidative stability and good cold flow properties. As a result, various systems and methods have been tested in order to achieve a selective partial hydrogenation of biodiesel’s FAMEs. In this review article, the catalytic systems and methods that stood out in various researches are presented and the factors that lead to the best possible outcome are investigated and discussed.